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Aliases for ZBED9 Gene

Aliases for ZBED9 Gene

  • Zinc Finger BED-Type Containing 9 2 3 5
  • Transposon-Derived Buster4 Transposase-Like Protein 3 4
  • Zinc Finger BED Domain-Containing Protein 9 3 4
  • Zinc Finger Protein 305 Pseudogene 2 2 3
  • SCAN Domain Containing 3 2 3
  • Zinc Finger Protein 452 2 3
  • ZNF305P2 3 4
  • Buster4 3 4
  • SCAND3 3 4
  • ZNF452 3 4
  • SCAN Domain-Containing Protein 3 3
  • DJ1186N24.3 3
  • KIAA1925 4
  • ZFP38-L 3

External Ids for ZBED9 Gene

Previous HGNC Symbols for ZBED9 Gene

  • ZNF305P2
  • ZNF452
  • SCAND3

Summaries for ZBED9 Gene

GeneCards Summary for ZBED9 Gene

ZBED9 (Zinc Finger BED-Type Containing 9) is a Protein Coding gene. GO annotations related to this gene include nucleic acid binding and protein dimerization activity. An important paralog of this gene is KRBA2.

Gene Wiki entry for ZBED9 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZBED9 Gene

Genomics for ZBED9 Gene

Regulatory Elements for ZBED9 Gene

Enhancers for ZBED9 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06G028647 1.1 ENCODE 6.5 -32.5 -32471 1.9 CREB3L1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF766 CBX5 ZNF143 ZKSCAN3 ZKSCAN4 ZKSCAN8 GPX5 ZSCAN9 ZBED9 TRT-CGT3-1 LINC00533 GC06M028665
GH06G028673 1.3 Ensembl ENCODE 5.1 -58.0 -58037 1.1 ATF1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 ZNF2 GTF3C2 FOS ZKSCAN3 ZNF603P ZKSCAN4 ZKSCAN8 GPX5 GPX6 ZBED9 TRA-CGC2-1 GC06M028676 PIR43008
GH06G028553 1.3 Ensembl ENCODE 4.6 +62.2 62202 1.5 HDGF PKNOX1 CREB3L1 ARNT YBX1 YY1 ZNF766 KLF13 ZHX2 MXD4 ZNF603P ZSCAN23 GPX5 OR2E1P COX11P1 ZBED9 TRR-TCG5-1 PIR44110 GC06M028544
GH06G028814 1 FANTOM5 5.1 -198.2 -198166 0.1 ATF1 PKNOX1 CREB3L1 ZNF2 ETS1 KLF7 REST ZNF518A ZNF592 KAT8 ZNF311 ZKSCAN3 ZFP57 ZBED9 ZNF602P OR14J1 GPX6 OR2W1 OR2J3 OR2B3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZBED9 on UCSC Golden Path with GeneCards custom track

Genomic Location for ZBED9 Gene

28,571,338 bp from pter
28,616,212 bp from pter
44,875 bases
Minus strand

Genomic View for ZBED9 Gene

Genes around ZBED9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZBED9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZBED9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZBED9 Gene

Proteins for ZBED9 Gene

  • Protein details for ZBED9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    SCAN domain-containing protein 3
    Protein Accession:
    Secondary Accessions:
    • Q2NKL9
    • Q5SRJ3
    • Q8TCN2
    • Q96MV9
    • Q96PW3

    Protein attributes for ZBED9 Gene

    1325 amino acids
    Molecular mass:
    151666 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ZBED9 Gene

Post-translational modifications for ZBED9 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for ZBED9 Gene

Domains & Families for ZBED9 Gene

Gene Families for ZBED9 Gene

Suggested Antigen Peptide Sequences for ZBED9 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZBED9: view

No data available for UniProtKB/Swiss-Prot for ZBED9 Gene

Function for ZBED9 Gene

Gene Ontology (GO) - Molecular Function for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IBA --
GO:0003700 transcription factor activity, sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with ZBED9: view
genes like me logo Genes that share phenotypes with ZBED9: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for ZBED9 Gene

Localization for ZBED9 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZBED9 gene
Compartment Confidence
nucleus 5
cytosol 2
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IBA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with ZBED9: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for ZBED9 Gene

Pathways & Interactions for ZBED9 Gene

SuperPathways for ZBED9 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZBED9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
GO:0015074 DNA integration IEA --
genes like me logo Genes that share ontologies with ZBED9: view

No data available for Pathways by source and SIGNOR curated interactions for ZBED9 Gene

Drugs & Compounds for ZBED9 Gene

No Compound Related Data Available

Transcripts for ZBED9 Gene

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZBED9 Gene

No ASD Table

Relevant External Links for ZBED9 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZBED9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZBED9 Gene

Protein differential expression in normal tissues from HIPED for ZBED9 Gene

This gene is overexpressed in Lung (45.5) and Placenta (23.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for ZBED9 Gene

Protein tissue co-expression partners for ZBED9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZBED9 Gene:


Evidence on tissue expression from TISSUES for ZBED9 Gene

  • Eye(4.2)
  • Nervous system(4.2)
genes like me logo Genes that share expression patterns with ZBED9: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZBED9 Gene

Orthologs for ZBED9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ZBED9 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SCAND3 34 35
  • 99.57 (n)
(Canis familiaris)
Mammalia SCAND3 34 35
  • 86.26 (n)
(Mus musculus)
Mammalia 2410018M08Rik 35
  • 32 (a)
(Anolis carolinensis)
Reptilia -- 35
  • 32 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC101733657 34
  • 51.36 (n)
(Danio rerio)
Actinopterygii BX664605.1 35
  • 34 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 27 (a)
Species where no ortholog for ZBED9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ZBED9 Gene

Gene Tree for ZBED9 (if available)
Gene Tree for ZBED9 (if available)

Paralogs for ZBED9 Gene

Paralogs for ZBED9 Gene

genes like me logo Genes that share paralogs with ZBED9: view

Variants for ZBED9 Gene

Sequence variations from dbSNP and Humsavar for ZBED9 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000132932 -- 28,616,829(+) GATCA(C/G)TGGAG upstream-variant-2KB
rs1000145115 -- 28,598,450(+) TCCCC(A/G)TCATG intron-variant
rs1000316884 -- 28,589,642(+) ATCAA(A/G)TTCAC intron-variant, upstream-variant-2KB
rs1000439885 -- 28,598,890(+) AAAAA(A/G)AAAAG intron-variant
rs1000480560 -- 28,605,047(+) CAGCT(C/T)CTCCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for ZBED9 Gene

Variant ID Type Subtype PubMed ID
dgv3296n106 CNV deletion 24896259
esv3576110 CNV gain 25503493
esv3608457 CNV gain 21293372
esv3608458 CNV gain 21293372
nsv1074388 CNV deletion 25765185
nsv601210 CNV gain 21841781
nsv830621 CNV gain 17160897

Variation tolerance for ZBED9 Gene

Residual Variation Intolerance Score: 27.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.90; 59.23% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZBED9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZBED9 Gene

Disorders for ZBED9 Gene

Relevant External Links for ZBED9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for ZBED9 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for ZBED9 Gene

Publications for ZBED9 Gene

  1. ZBED evolution: repeated utilization of DNA transposons as regulators of diverse host functions. (PMID: 23533661) Hayward A. … Jern P. (PLoS ONE 2013) 2 3 4 64
  2. On the transposon origins of mammalian SCAND3 and KRBA2, two zinc-finger genes carrying an integrase/transposase domain. (PMID: 23550032) Llorens C. … Moya A. (Mob Genet Elements 2012) 2 3 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall A.J. … Beck S. (Nature 2003) 3 4 64

Products for ZBED9 Gene

Sources for ZBED9 Gene

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